Nextflow Registry | nf-core/snpeff/snpeff@0.0.0-6c4ed3a

nf-core/snpeff/snpeff @ 0.0.0-6c4ed3a

Genetic variant annotation and functional effect prediction toolbox

annotation effect prediction snpeff variant vcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @maxulysse

Maintainers: @maxulysse

Genetic variant annotation and functional effect prediction toolbox

Add the following snippet to your workflow script to include this module.

include { SNPEFF_SNPEFF } from 'nf-core/snpeff/snpeff'

MIT License

Process

`Name`	`SNPEFF_SNPEFF`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf` file	vcf to annotate

`db` string	which db to annotate with

#3 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`cache` file	path to snpEff cache (optional)

Output 5 channels

#1 vcf tuple

`meta` file	annotated vcf `*.ann.vcf`
`*.ann.vcf` file	annotated vcf `*.ann.vcf`

#2 report tuple

#3 genes_txt tuple

`meta` file	annotated vcf `*.ann.vcf`
`${task.process}` string	The process
`snpeff` string	The tool name
`*.genes.txt` file	txt (tab separated) file having counts of the number of variants affecting each transcript and gene `*.genes.txt`

#4 summary_html tuple

`meta` file	annotated vcf `*.ann.vcf`
`${task.process}` string	The process
`snpeff` string	The tool name
`*.html` file	snpEff summary statistics in html file `*.html`

#5 versions_snpeff tuple

`${task.process}` string	The process the versions were collected from
`snpeff` string	The tool name
`snpEff -version 2>&1 \| cut -f 2 -d ' '` string	The command used to generate the version of the tool

Tool	Description	Homepage
snpeff	SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).	https://pcingola.github.io/SnpEff/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:46:41 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsnpeff%2Fsnpeff/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/snpeff/snpeff/blobs/sha256:082068174a7d6963119e0225b51785374a519c2b6d8512e292195c32ba4c3c7c